chrX-76428384-GTGCCGCCCACCGCCTCTGAGGTACCGAGCACCTCCC-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2
The NM_020932.3(MAGEE1):c.466_501delGCCTCTGAGGTACCGAGCACCTCCCTGCCGCCCACC(p.Ala156_Thr167del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 112,817 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_020932.3 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000239 AC: 27AN: 112768Hom.: 0 Cov.: 26 AF XY: 0.000143 AC XY: 5AN XY: 35024
GnomAD3 exomes AF: 0.000266 AC: 48AN: 180282Hom.: 0 AF XY: 0.000242 AC XY: 16AN XY: 66216
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000484 AC: 531AN: 1097746Hom.: 0 AF XY: 0.000460 AC XY: 167AN XY: 363390
GnomAD4 genome AF: 0.000239 AC: 27AN: 112817Hom.: 0 Cov.: 26 AF XY: 0.000143 AC XY: 5AN XY: 35083
ClinVar
Submissions by phenotype
not provided Benign:1
MAGEE1: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at